Bio::G...:Markup(3pm)

📦
version 2.56 · 5 versions
, in ubuntu questing

💖 Bio::G...:Markup(3pm) 💖

okay bestie, so this is Bio::Graphics::Browser2::Markup — the Perl doc page for it, straight out of the User Contributed Perl Documentation collection, and it's literally all about marking up sequences in text form. no cap. 🎀

✨ NAME ✨

Bio::Graphics::Browser2::Markup — Markup routines for sequences in text form 🦋

🌸 VERSION (CVS-info) 🌸

so it's a CVS-checked-out situation, the vibe is very "old money repository":

$RCSfile: Markup.pm,v $
$Revision$
$Author: lstein $
$Date: 2008-09-09 20:53:36 $

💅 SYNOPSIS 💅

here's the whole moment, in code, untouched, exactly as the ancestors wrote it:

use Bio::Graphics::Browser2::Markup;

my $string = join '','a'..'z','a'..'z','a'..'z';
my $markup = Bio::Graphics::Browser2::Markup->new;

$markup->add_style(cds=>'UPPERCASE');
$markup->add_style(exon     =>'Text-decoration: underline');
$markup->add_style(variation=>'Font-weight: bold');
$markup->add_style(italic=>'Font-style: oblique');
$markup->add_style(yellow=>'BGCOLOR blue');
$markup->add_style(green=>'BGCOLOR red');
$markup->add_style(orange=>'BGCOLOR orange');
$markup->add_style(mango=>'FGCOLOR red');
$markup->add_style(br=>'<br>');
$markup->markup(\$string,[
                         ['cds',1=>10],
                         ['cds',12=>15],
                         ['variation',20=>41],
                         ['exon',0=>29],
                         ['exon',32=>40],
                         ['italic',18=>29],
                         ['yellow',5=>40],
                         ['green',20=>50],
                         ['orange',30=>60],
                         ['mango',0=>36],
                         ['br',10=>10],
                         ['br',20=>20],
                         ['br',30=>30],
                         ['br',40=>40],
                         ['br',50=>50],
                         ['br',60=>60],
                         ]);
print $string,"\n";

👑 DESCRIPTION 👑

This module marks up a string with HTML cascading stylesheet styles in such a way that intersecting regions contain the union of the two intersecting styles. 🫶

It also handles colors in such a way that intersecting colors are added up. slay.

🌈 METHODS 🌈

💜 $annotator = Bio::Graphics::Browser2::Markup->new

Create a new Markup object. fresh, new, main character energy. ✨

💜 $old_style = $annotator->add_style($symbolic_name=>$style)

Add an annotation style.

$symbolic name is a unique identifier to be used for ornamenting the string. yes bestie, a little name tag for your style.

$style is one of:

- a CSS/2 stylesheet entry of form "style: value"
- the word   "UPPERCASE"         (make uppercase)
- the word   "LOWERCASE"         (make lowercase)
- the phrase "FGCOLOR #RRGGBB"   (foreground color)
- the phrase "FGCOLOR color-name"
- the phrase "BGCOLOR #RRGGBB"   (background color)
- the phrase "BGCOLOR color-name"
- an HTML tag, indicated by a leading "E<lt>" character
- anything else, will be inserted blindly

When calculating intersected regions, styles will be aggregated, upper and lowercasing will be performed directly on the data, colors will be additive, and HTML will be inserted blindly. (yes, blindly. it's giving chaos but make it fashion. 🙈)

an invalid color name will cause this module to die. 😭 literally die. so here's how you get the valid color names, bestie, so you don't have to find out the hard way:
perl -MBio::Graphics::Panel \
     -e 'print join "\n",sort Bio::Graphics::Panel->color_names'

💜 $style = $annotator->style($symbolic_name)

Get the style corresponding to symbolic name, or undef if the name is unrecognized. (unrecognized = ghosted. 💀)

💜 $style = $annotator->get_style($symbolic_name)

Get a list of CSS/2 styles corresponding to symbolic name. Will die if the name is not recognized or does not correspond to an entry of type "style". no vibes, just death. 😭

💜 $flag = $annotator->valid_symbol($symbolic_name)

Return true if the symbolic name is valid. simple. iconic. no notes. ✅

💜 $result = $annotator->markup(\$sequence,\@annotated_regions)

Mark up the string referenced by $sequence, according to the regions contained in $annotated_regions.

  • $sequence is a scalar ref, which will be modified in place (make a copy of it if you need to). ⚠️
  • $annotated_regions is a arrayref to the following list:
([symbolic_name,start,end], [symbolic_name,start,end], ....)

The result indicates whether the markup was successful.

IMPORTANT: Regions are numbered using space-oriented coordinates, which means that start=0 means to insert in front of the first base pair, and an end equal to the sequence length will insert after the last base pair:
  0 1 2 3 4 5 6 7     perl string coordinates
  1 2 3 4 5 6 7 8     sequence coordinates
  g a t c g a t c     sequence
  0 1 2 3 4 5 6 7 8    space coordinates
 To select first base:                    start=0, end=1
 To insert markup between bases 1 and 2:  start=1, end=1
 To select last base:                     start=7, end=8
 To select entire sequence:               start=0, end=8

This means that some munging of the sequence annotation must be performed, but it keeps the notation unambiguous. 💅 worth it.

🦋 Internal Methods (not for external use; documentation incomplete) 🦋

okay so, backstage area only — not for external use, and the docs are incomplete, so we're all just vibing off the signatures here.
@events = $annotator->_add_colors($style_tag,$regions)
$style_symbol = $annotator->_add_colors($style_tag,$regions)
$color = $annotator->_add_color($color1,$color2)
$color = $annotator->_subtract_color($color1,$color2)
$html_color = $annotator->_to_html_color($color)
@tag_positions = $annotator->_unify($region_definitions)
$style_fragment = $annotator->_to_style($symbols)
@tag_positions = $annotator->_linearize_html($region_definitions)
\@events = $annotator->_regions_to_events($regions)
    turn a series of regions into a series of start and end events
    because of the problem of events that start/stop in the same place
    each event also gets a sequence that can be used to keep events
    matched in a nested way

$annotator->_add_markup($string_to_modify,$tag_positions)

🔥 SEE ALSO 🔥

go read these next bestie, they're the extended universe:

  • Bio::Graphics::Panel
  • Bio::Graphics::Glyph
  • Bio::Graphics::Feature
  • Bio::Graphics::FeatureFile
  • Bio::Graphics::Browser
  • Bio::Graphics::Browser2::Plugin

🌸 AUTHOR 🌸

Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2002 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. 🫶

okay and that's the whole page bestie, love that for us 💖 this was perl v5.40.0, dated 2024-10-20, and you just read Bio::G...:Markup(3pm) — periodt. 👑✨

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